It is also possible that there is an invalid string in the genepix file.

https://stat.ethz.ch/pipermail/bioc-devel/2006-March/000420.html and related
posts

have some relevant information

On Mon, Apr 5, 2010 at 10:51 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> Hi Luis --
>
> On 04/05/2010 09:10 AM, lapereir@uc.cl wrote:
> > HI!!
> >
> > I am sorry, i read the posting guide but for some reason i dont read that
> > requirement. So here i write the output of sessionInfo(), also include
> the
> > traceback() ouput and Sys.getlocale().
> >
> >> Sys.getlocale()
> > [1] "en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8"
>
> I think the suggestion was to change this like
>
> > Sys.setlocale(locale="C")
> [1]
>
> "LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C"
>
> I think this will work on your operating system, but it may be necessary
> to start R in the correct locale.
>
> Martin
>
>
> >> traceback()
> > 6: gsub("\\.", "\\\\.", x)
> > 5: protectMetachar(allcnames[i])
> > 4: grep(protectMetachar(allcnames[i]), text.to.search)
> > 3: read.columns(fullname, required.col, text.to.search, skip = skip,
> >        sep = sep, quote = quote, stringsAsFactors = FALSE, fill = TRUE,
> >        flush = TRUE, ...)
> > 2: switch(source2, quantarray = {
> >        firstfield <- scan(fullname, what = "", sep = "\t", flush = TRUE,
> >            quiet = TRUE, blank.lines.skip = FALSE, multi.line = FALSE,
> >            allowEscapes = FALSE)
> >        skip <- grep("Begin Data", firstfield)
> >        if (length(skip) == 0)
> >            stop("Cannot find \"Begin Data\" in image output file")
> >        nspots <- grep("End Data", firstfield) - skip - 2
> >        obj <- read.columns(fullname, required.col, text.to.search,
> >            skip = skip, sep = sep, quote = quote, stringsAsFactors =
> FALSE,
> >            fill = TRUE, nrows = nspots, flush = TRUE, ...)
> >    }, arrayvision = {
> >        skip <- 1
> >        cn <- scan(fullname, what = "", sep = sep, quote = quote,
> >            skip = 1, nlines = 1, quiet = TRUE, allowEscape = FALSE)
> >        fg <- grep(" Dens - ", cn)
> >        if (length(fg) != 2)
> >            stop(paste("Cannot find foreground columns in", fullname))
> >        bg <- grep("^Bkgd$", cn)
> >        if (length(bg) != 2)
> >            stop(paste("Cannot find background columns in", fullname))
> >        columns <- list(R = fg[1], Rb = bg[1], G = fg[2], Gb = bg[2])
> >        obj <- read.columns(fullname, required.col, text.to.search,
> >            skip = skip, sep = sep, quote = quote, stringsAsFactors =
> FALSE,
> >            fill = TRUE, flush = TRUE, ...)
> >        fg <- grep(" Dens - ", names(obj))
> >        bg <- grep("^Bkgd$", names(obj))
> >        columns <- list(R = fg[1], Rb = bg[1], G = fg[2], Gb = bg[2])
> >        nspots <- nrow(obj)
> >    }, bluefuse = {
> >        skip <- readGenericHeader(fullname, columns = c(columns$G,
> >            columns$R))$NHeaderRecords
> >        obj <- read.columns(fullname, required.col, text.to.search,
> >            skip = skip, sep = sep, quote = quote, stringsAsFactors =
> FALSE,
> >            fill = TRUE, flush = TRUE, ...)
> >        nspots <- nrow(obj)
> >    }, genepix = {
> >        h <- readGPRHeader(fullname)
> >        if (verbose && source == "genepix.custom")
> >            cat("Custom background:", h$Background, "\n")
> >        skip <- h$NHeaderRecords
> >        obj <- read.columns(fullname, required.col, text.to.search,
> >            skip = skip, sep = sep, quote = quote, stringsAsFactors =
> FALSE,
> >            fill = TRUE, flush = TRUE, ...)
> >        nspots <- nrow(obj)
> >    }, smd = {
> >        skip <- readSMDHeader(fullname)$NHeaderRecords
> >        obj <- read.columns(fullname, required.col, text.to.search,
> >            skip = skip, sep = sep, quote = quote, stringsAsFactors =
> FALSE,
> >            fill = TRUE, flush = TRUE, ...)
> >        nspots <- nrow(obj)
> >    }, {
> >        skip <- readGenericHeader(fullname, columns = columns, sep =
> > sep)$NHeaderRecords
> >        obj <- read.columns(fullname, required.col, text.to.search,
> >            skip = skip, sep = sep, quote = quote, stringsAsFactors =
> FALSE,
> >            fill = TRUE, flush = TRUE, ...)
> >        nspots <- nrow(obj)
> >    })
> > 1: read.maimages(targets, source = "genepix", wt.fun = f)
> >
> >> sessionInfo()
> > R version 2.10.0 (2009-10-26)
> > i386-apple-darwin9.8.0
> >
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] limma_3.2.1
> >
> > Well, sorry for the extention, but hopefully i cant get an anwser and if
> this
> > not the
> >
> > Greets
> >
> >
> >
> > Vincent Carey escribió:
> >> Please read the posting guide.  You did not provide the result of
> >> sessionInfo().  You may be using an inconvenient locale.  Typically if
> the
> >> following holds
> >>
> >>> Sys.getlocale()
> >> [1] "C"
> >>
> >> you will not run into the error noted for this task.
> >>
> >> On Sun, Apr 4, 2010 at 9:31 PM, <lapereir@uc.cl> wrote:
> >>
> >>> Dear list
> >>>
> >>> I am getting a couple of erros when trying to  import gpr files using
> the
> >>> read.maimages of Limma.
> >>>
> >>>> targets<-readTargets("targets.txt")
> >>>> RG <- read.maimages(targets, source="genepix", wt.fun=f)
> >>> Error in gsub("\\.", "\\\\.", x) :
> >>> input string 1 is invalid in this locale
> >>>
> >>> I search in R Help for the function of gsub, but i cannot fix the error
> >>> that
> >>> give me, so that i cant import any genepix (.gpr) files.
> >>>
> >>> Thank
> >>> Luis
> >>>
> >>> _______________________________________________
> >>> Bioconductor mailing list
> >>> Bioconductor@stat.math.ethz.ch
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>> Search the archives:
> >>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>
> >>
> >
> >
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>

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